User:Eric Martz/Sandbox 8

Chemistry of Water and Its Hydrogen Bonds
Prepared in collaboration with User:Gabriel Pons.

One Molecule



 * (restore initial scene )
 * partial charge values
 * shape of the molecule (spacefilling) (van der Waals radii)
 * translucent surface colored by molecular electrostatic potential Positive (+), Negative (-)

Technical Information
The following scene demonstrates a problem with greek letters in labels in Jmol
 * partial charges (using &delta; in the label, it gets corrupted)

Script for translucent MEP colored surface: {hydrogen}.partialCharge = 0.41 {oxygen}.partialCharge = -0.82

isosurface resolution 6 MOLECULAR map MEP
 * 1) IMPORTANT: the SOLVENT version of isosurface
 * 2) IGNORES WATER UNCONDITIONALLY! We must us MOLECULAR!
 * 3) isosurface resolution 6 MOLECULAR colorscheme "rwb" map MEP
 * 1) Higher values of resolution make a choppier surface that rotates
 * 2) more jerkily. 6 is good.

color isosurface "rwb" range -0.2 0.2
 * 1) chose this range by trial and error.
 * 2) default is -0.1 0.1 as reported by the isosurface command.

color isosurface translucent 2


 * 1) or the partial charges could be in the PDB file using
 * 2) this command to transfer the values.
 * 3) {*}.partialCharge = {*}.temperature.all

Possible script for large translucent hbonds: select all calculate hbonds hbonds 0.3 color hbonds white color hbonds translucent 6